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methylationepic
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Beta values and M values cluster differently
methylationEPIC
minfi
microarray
epigenetics
EPIC
4.5 years ago
rmf
▴ 20
0
votes
0
replies
656
views
Best normalisation method
microarray
methylationEPIC
epigenetics
minfi
EPIC
4.5 years ago
rmf
▴ 20
3
votes
6
replies
1.7k
views
could not find function "champ.load"
ChAMP
champ 2.9.10
methylationepic
5.5 years ago
david.ch
• 0
0
votes
0
replies
856
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
5.6 years ago
gabrielrfries
• 0
0
votes
1
reply
1.6k
views
ChAMP Methylation analysis error code "could not find function champ.load"
champ
methylationepic
updated 5.7 years ago by
Yuan Tian
▴ 270 • written 5.7 years ago by
csappleby-mallinder1
• 0
3
votes
4
replies
2.5k
views
Error while using champ.svd() function in subset of data
ChAMP
methylationepic
epicarray
epigenomics
updated 6.0 years ago by
rcavalca
▴ 140 • written 6.0 years ago by
karthikrpad
▴ 10
0
votes
0
replies
764
views
Error when changing the database for minfi dropLociWithSnps
minfi
methylationepic
illuminahumanmethylationepicanno.ilmn10b.hg19
SNP
6.2 years ago
Ellen O
• 0
0
votes
2
replies
1.6k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 6.4 years ago by
Guido Hooiveld
★ 3.7k • written 6.4 years ago by
Ellen O
• 0
0
votes
4
replies
1.4k
views
minfi "mapToGenome" dimension error
methylation
epic microarray
minfi
methylationepic
6.6 years ago
nhejazi
• 0
0
votes
0
replies
869
views
Shinymethyl 850K Array quality control signal cutoffs
shinymethyl
minfi
epic microarray
methylationepic
qualitycontrol
6.6 years ago
chelsey.ju
• 0
0
votes
3
replies
1.3k
views
MINFI missing samples in qcreports and densityplots
minfi
illumina
methylationEPIC
densityplot
6.7 years ago
annabelle.congras
▴ 10
11 results • Page
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Replies
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of
by
Gregory
• 0
Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …
Comment: DiffBind handling of replicates and consensus
by
Rory Stark
★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles)
by
Rory Stark
★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles)
by
Dorien
▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Votes
Comment: DiffBind: dba.plotProfile(profiles)
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
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